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The efficiency of the microwave-assisted extraction (MAE) technique on recovering nutritional and bioactive oils from salmon (Salmo salar) side streams was evaluated and compared to Soxhlet extraction. The response surface methodology (RSM) coupled with a central composite rotatable design was used to optimize time, microwave power, and solid/liquid ratio of the MAE process in terms of oil yield. The optimal MAE conditions were 14.6 min, 291.9 W, 80.1 g/L for backbones, 10.8 min, 50.0 W, 80.0 g/L for heads, and 14.3 min, 960.6 W, 99.5